As has been said, as long as they're part of the same Exchange Organization you can have a single BES.

If you're doing something like HMC, make sure you're an Alliance Partner, read through the HMC docs, and then give the Administration Guide a review ... it talks about hosted and / or multi domain support.

The key is, all Exchange servers that talk to a given BES need to be a part of the same Exchange Organzation.